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    50 repositories

    • toil

      Public
      A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.
      Python
      •
      Apache License 2.0
      •240•0•0•2•Updated Dec 13, 2024Dec 13, 2024

    • CaVEMan

      Public
      SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib
      C
      •
      GNU Affero General Public License v3.0
      •13•0•0•0•Updated Dec 10, 2024Dec 10, 2024

    • isabl_cli

      Public
      🤖 isabl Command Line Client and SDK.
      Python
      •
      Other
      •3•3•18•3•Updated Dec 10, 2024Dec 10, 2024

    • toil_container

      Public
      🐳 Toil + Docker and Singularity.
      Python
      •
      MIT License
      •6•9•3•0•Updated Nov 22, 2024Nov 22, 2024

    • nf-purple

      Public
      Nextflow Pipeline to run Purple from HmfTools
      Nextflow
      •0•0•0•1•Updated Nov 16, 2024Nov 16, 2024

    • Complex_Oncoprint

      Public
      R
      •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

    • ipssm-api

      Public
      API and CLI for IPSS-M
      HTML
      •
      Other
      •0•0•1•0•Updated Nov 1, 2024Nov 1, 2024

    • docker-annotsv

      Public
      Dockerfile for lgmgeo/AnnotSV tool
      Dockerfile
      •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024

    • register_apps

      Public
      👾 Register versioned toil container pipelines in a bin directory as singularity images.
      Python
      •
      MIT License
      •0•6•1•1•Updated May 30, 2024May 30, 2024

    • mergeSVvcf

      Public
      Python package and routines for merging SV VCF files
      Python
      •
      MIT License
      •10•7•0•1•Updated May 23, 2024May 23, 2024

    • hileup

      Public
      horizontal pileup
      C
      •
      Apache License 2.0
      •3•0•0•0•Updated Jan 16, 2024Jan 16, 2024

    • Asimomitis_ACM_2023

      Public
      ICBBB 2023: Predicting Single Cell Genotypes from Single Cell Expression Profiles in AML Using Deep Learning
      Python
      •0•0•0•0•Updated Nov 21, 2023Nov 21, 2023

    • docker-hmftools

      Public
      🐳 Docker container with several HMF tools installed
      Dockerfile
      •0•0•0•0•Updated Sep 5, 2023Sep 5, 2023

    • Gao_NC_CH

      Public
      Code and Data for Gao et al., Nature Communications 2021
      Jupyter Notebook
      •2•6•0•0•Updated Aug 16, 2023Aug 16, 2023

    • Domenico_Asimomitis_ICML_2023

      Public
      Code accompanying "High-Resolution Interpretable Classification of Artifacts versus Real Variants in Whole Genome Sequencing Data from Archived Tissue" by Domenico & Asimomitis et al. https://icml-compbio.github.io/2023/papers/WCBICML2023_paper116.pdf
      Jupyter Notebook
      •1•1•0•0•Updated Aug 9, 2023Aug 9, 2023

    • papaemmelab

      Public template
      👩🏻‍🔬 The Papaemmanuil Lab Website
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •317•0•0•0•Updated Aug 7, 2023Aug 7, 2023

    • toil_hla

      Public
      🧬 Toil workflow for HLA typing tools.
      Python
      •
      MIT License
      •0•0•0•0•Updated May 23, 2023May 23, 2023

    • IPSSMstudy

      Public
      IPSS-M study
      HTML
      •0•10•0•0•Updated Apr 3, 2023Apr 3, 2023

    • Shukla_Levine_Gundem

      Public
      Data for Shukla, Levine, Gundem et al.
      Jupyter Notebook
      •1•5•0•0•Updated Apr 3, 2023Apr 3, 2023

    • cnvkit

      Public
      Copy number variant detection from targeted DNA sequencing
      Python
      •
      Other
      •166•0•0•0•Updated Mar 16, 2023Mar 16, 2023

    • ipssm

      Public
      Molecular International Prognostic Scoring System IPSS-M for Myelodysplastic Syndromes
      R
      •
      Other
      •5•8•1•0•Updated Feb 5, 2023Feb 5, 2023

    • Tazi_NatureC_AML

      Public
      Github Repository for Tazi et al. : Unified classification and risk-stratification in Acute Myeloid Leukemia. Please check our online tool : https://www.aml-risk-model.com/
      Jupyter Notebook
      •6•5•0•0•Updated Aug 9, 2022Aug 9, 2022

    • lsf

      Public
      Snakemake profile for running jobs on an LSF cluster
      Python
      •
      MIT License
      •22•0•0•0•Updated Jul 12, 2022Jul 12, 2022

    • MDS_SF3B1_iPSC

      Public
      Repository of Asimomitis et al. Blood Advances publication: Patient-specific MDS-RS iPSCs define the mis-spliced transcript repertoire and chromatin landscape of SF3B1-mutant HSPCs (https://doi.org/10.1182/bloodadvances.2021006325)
      Jupyter Notebook
      •0•1•0•0•Updated Mar 16, 2022Mar 16, 2022

    • MDS-TP53-state

      Public
      TP53 allelic state in MDS
      HTML
      •4•4•0•0•Updated Feb 4, 2022Feb 4, 2022

    • cookiecutter-toil

      Public
      🍪 Cookiecutter template for Class Based Toil pipelines.
      Python
      •
      MIT License
      •1•4•0•0•Updated Dec 2, 2021Dec 2, 2021

    • split_bed_by_index

      Public
      Split bed intervals by estimated read counts from bam index
      Nim
      •
      MIT License
      •0•9•2•1•Updated Nov 15, 2021Nov 15, 2021

    • toil_example

      Public
      🤖 A Toil example pipeline created with cookiecutter-toil.
      pipelinestoiltravis-badgecodecov-badgepypi-badge
      Python
      •
      MIT License
      •1•0•0•0•Updated Sep 8, 2021Sep 8, 2021

    • split_bed_by_reads

      Public
      Split bed intervals by maximum read counts
      nim
      Nim
      •
      MIT License
      •0•9•0•0•Updated Jul 14, 2021Jul 14, 2021

    • docker-cellranger

      Public
      Dockerfile to create a cellranger container
      Dockerfile
      •0•0•0•0•Updated Apr 23, 2021Apr 23, 2021